Also the entirety of Metropolis Part II: Scenes From A Memory.
"Overture 1928", while not the longest or flashiest song technically, does an amazing job of mashing up the melodies of the other songs on the album in a way that feels completely natural and is completely unnoticeable.
"The Dance of Eternity", which has one hundred and six time signature changes in six minutes. Both Myung and Portnoy deserve mention.
"Six Degrees of Inner Turbulence": One song, eight parts and 42 minutes of awesome. For maximum awesomeness, listen to all of the parts non-stop (if necessary, take a music-editing program and edit all the song parts together) for an absolutely epic joyride.
Off that album "The Glass Prison" deserves a special mention. The intro alone - which is admittedly quite long, but it is Dream Theater - is more awesome than some bands cram into one album.
The second act of their 20th anniversary concert features them playing with a full symphony orchestra. If you think DT isn't awesome per se, then wait until you hear "Six Degrees Of Inner Turbulence" and "Octavarium".
And for that matter, "Metropolis". It is the greatest possible way to finish an album ever.
"In the Presence of Enemies", both parts.
"Constant Motion", one of Dream Theater's few singles, combines the speed of thrash metal with the technicality that is their hallmark, with a refrain worthy of power metal. "Forevermore! Into the night, blistering!"